User: JD

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JD10
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3 years, 4 months ago
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3 years, 10 months ago
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j***************@hms.harvard.edu

Posts by JD

<prev • 7 results • page 1 of 1 • next >
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Combining compareCluster with enricher in clusterProfiler
... Hello,  In the tutorial for clusterProfiler, it mentions that the universal enricher function can be combined with the biological theme compareCluster function: "The comparison function was designed as a framework for comparing gene clusters of any kind of ontology associations, not onlygroupGO, e ...
clusterprofiler written 3.4 years ago by JD10 • updated 3.4 years ago by Guangchuang Yu1.1k
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Comment: C: Diffbind - retrieving individual sample RPKM values for differentially bound sit
... That definitely helps. Thank you so much Rory! ...
written 3.7 years ago by JD10
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Comment: C: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
... Hi Tom,  Thanks again for the useful information. I will try the samtools method. This is actually an ATAC-seq experiment, my first one. My -seq experience thus far has been exclusively with ChIP-seq and I agree with you, generally no need to do paired-end. Otherwise, I've been using a similar anal ...
written 3.8 years ago by JD10
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Answer: A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
... Hi Tom,  Thanks for your helpful and quick response. I'm now extracting the counts using your steps and then tacking a column for total reads onto the GR object to do the rpm calculation. It is working perfectly and exactly what I was looking for.  One more quick question - my .bam files are paire ...
written 3.8 years ago by JD10
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Comment: C: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
... Hi Rory,  Thanks for the quick reply. I'll go the Bioconductor route.  ...
written 3.8 years ago by JD10
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ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
... Hello all, I am looking for advice on the best way to count the number of reads in each peak of a bed file on a  sample-by-sample basis, rather than from a consensus peak set. In other words, I have a peak file and bam file for sample 1 and I want to be able to count reads in each peak, normalize b ...
diffbind chipqc written 3.8 years ago by JD10
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Diffbind - retrieving individual sample RPKM values for differentially bound sites
... Hello -  I have run a dba analysis on 4 cell types, each with 2 replicates. The way I've setup the call to dba.analyze  results in 10 contrasts. I have two questions about retrieving the results: 1) Is it possible to retrieve the DB peaks from an individual contrast, with the score column reported f ...
diffbind written 3.9 years ago by JD10 • updated 3.7 years ago by Rory Stark2.9k

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Diffbind - retrieving individual sample RPKM values for differentially bound sites
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Diffbind - retrieving individual sample RPKM values for differentially bound sites

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